Author: | |
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Release: | $Id$ |
Date: | December 09, 2013 |
Tags: | Python |
I tried the Biopython parser, but it was too slow for large genomic chunks.
index file/files.
Two new files are create - db_name.fasta and db_name.idx
check if a certain file has been indexed.
get genomic fragment.
split a fasta file into a subset of files.
If pattern is not given, random file names are chosen.
return a converter function for converting various coordinate schemes into 0-based, both strand, closed-open ranges.
converter functions have the parameters x, y, s, l: with x and y the coordinates of a sequence fragment, s the strand (True is positive) and l being the length of the contig.